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Sample GSM348419 Query DataSets for GSM348419
Status Public on Jul 19, 2011
Title GAS_DIS_GC_YG74T_C2
Sample type RNA
 
Source name Primary gastric cancer
Organism Homo sapiens
Characteristics gastric adenocarcinoma
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer's protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)
Label Biotin
Label protocol Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina?? TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)
 
Hybridization protocol Labeled, amplified material (1,500 ng per array) was hybridized to a ver. 3 of the Illumina Human-6 BeadChip (48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual
Scan protocol Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions
Description To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48804 probes on the Human-6 beadChip ver. 3 were used. Clinical data provided as a supplementary file on Series record: GSE13861_GE_MDACC_DepSysB_ClinicalInformation.xls.gz
Data processing Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformation. To export to a data matrix, Sample Gene Profile option of this software was used.
 
Submission date Dec 08, 2008
Last update date Jul 19, 2011
Contact name Sangbae Kim
E-mail(s) sangbkim22@gmail.com
Organization name Baylor Colleage of Medicine
Department HGSC
Street address 1 Baylor plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL6884
Series (1)
GSE13861 Gene expression signature-based novel prognostic risk score in gastric cancer

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
ILMN_1809034 6.29315
ILMN_1660305 7.481073
ILMN_1792173 6.944741
ILMN_1762337 5.804776
ILMN_2055271 5.527633
ILMN_1736007 5.340206
ILMN_1814316 5.311794
ILMN_2359168 5.515384
ILMN_1731507 5.29315
ILMN_1787689 5.418865
ILMN_1745607 12.718008
ILMN_2136495 5.107688
ILMN_1668111 5.377818
ILMN_2295559 5.20085
ILMN_1735045 7.345272
ILMN_1680754 5.380245
ILMN_2375184 5.471187
ILMN_1659452 5.602588
ILMN_1767388 5.493135
ILMN_1675204 5.125155

Total number of rows: 48803

Table truncated, full table size 1045 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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